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    SDCBP syndecan binding protein [ Homo sapiens (human) ]

    Gene ID: 6386, updated on 4-Feb-2024

    Summary

    Official Symbol
    SDCBPprovided by HGNC
    Official Full Name
    syndecan binding proteinprovided by HGNC
    Primary source
    HGNC:HGNC:10662
    See related
    Ensembl:ENSG00000137575 MIM:602217; AllianceGenome:HGNC:10662
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    ST1; MDA9; SYCL; MDA-9; SDCBP1; TACIP18
    Summary
    The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Jan 2017]
    Expression
    Ubiquitous expression in placenta (RPKM 77.0), gall bladder (RPKM 73.7) and 25 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See SDCBP in Genome Data Viewer
    Location:
    8q12.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (58553261..58582858)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (58974408..59004011)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (59465820..59495417)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr8:59404317-59405516 Neighboring gene CYP7A1 5' regulatory region Neighboring gene cytochrome P450 family 7 subfamily A member 1 Neighboring gene peptidylprolyl isomerase A pseudogene 85 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:59465479-59466196 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr8:59507186-59508385 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 27412 Neighboring gene neutral sphingomyelinase activation associated factor Neighboring gene ribosomal protein S26 pseudogene 7 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:59558003-59558563 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:59563765-59564489 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:59570852-59571415 Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:59571416-59571978 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19219 Neighboring gene small nucleolar RNA U13

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Syntenin-1 is recruited toward HIV-1 gp120/gp41-driven virus/cell and cell/cell contacts, associates with CD4, limits HIV-1-induced cell fusion and viral entry, and modulates gp120/gp41-triggered actin polymerization and PIP2 accumulation PubMed
    env Genes, including GABRP, ADF, HINT, PRSS2, SDCBP, PTK9, PPP2R5B, ITGA3, PRKCBP1, HMOX2, HAT1, PPP1cB, and ICAM-1, are upregulated after treatment of human astrocytes with HIV-1 gp120 PubMed
    Envelope transmembrane glycoprotein gp41 env Syntenin-1 is recruited toward HIV-1 gp120/gp41-driven virus/cell and cell/cell contacts, associates with CD4, limits HIV-1-induced cell fusion and viral entry, and modulates gp120/gp41-triggered actin polymerization and PIP2 accumulation PubMed
    Nef nef HIV-1 Nef inhibits the expression of syndecan binding protein (syntenin) in human podocyte PubMed
    matrix gag HIV-1 MA is identified to have a physical interaction with syndecan binding protein (SDCBP) in human HEK293 and/or Jurkat cell lines by using affinity tagging and purification mass spectrometry analyses PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cell adhesion molecule binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables cytoskeletal anchor activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    enables ephrin receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables frizzled binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables growth factor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables identical protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables interleukin-5 receptor binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    enables ionotropic glutamate receptor binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables neurexin family protein binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables phosphatidylinositol-4,5-bisphosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein heterodimerization activity IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein sequestering activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-containing complex binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables syndecan binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables syndecan binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables syndecan binding NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in Ras protein signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in actin cytoskeleton organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in chemical synaptic transmission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in intracellular signal transduction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of receptor internalization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in negative regulation of transcription by RNA polymerase II IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of JNK cascade IC
    Inferred by Curator
    more info
    PubMed 
    involved_in positive regulation of cell growth IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell migration IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of cell population proliferation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of epithelial to mesenchymal transition IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of extracellular exosome assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of phosphorylation IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in positive regulation of transforming growth factor beta receptor signaling pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of transforming growth factor beta receptor signaling pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in presynapse assembly IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein targeting to membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in substrate-dependent cell migration, cell extension NAS
    Non-traceable Author Statement
    more info
    PubMed 
    Component Evidence Code Pubs
    located_in adherens junction NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in azurophil granule lumen TAS
    Traceable Author Statement
    more info
     
    located_in blood microparticle HDA PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoskeleton NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    located_in endoplasmic reticulum membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in extracellular space HDA PubMed 
    located_in extracellular vesicle HDA PubMed 
    located_in focal adhesion IEA
    Inferred from Electronic Annotation
    more info
     
    part_of interleukin-5 receptor complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    PubMed 
    located_in melanosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nuclear membrane IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in presynapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    syntenin-1
    Names
    melanoma differentiation associated protein-9
    pro-TGF-alpha cytoplasmic domain-interacting protein 18
    scaffold protein Pbp1
    syndecan binding protein (syntenin)
    syndecan-binding protein 1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_001007067.2NP_001007068.1  syntenin-1 isoform 1

      See identical proteins and their annotated locations for NP_001007068.1

      Status: REVIEWED

      Source sequence(s)
      BC013254, BG772269, U83463
      Consensus CDS
      CCDS6172.1
      UniProtKB/Swiss-Prot
      B2R5Q7, B4DUH3, B7ZLN2, O00173, O00560, O43391, Q14CP2
      UniProtKB/TrEMBL
      B4DQ93
      Related
      ENSP00000411771.2, ENST00000413219.6
      Conserved Domains (1) summary
      cd00992
      Location:112191
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    2. NM_001007068.2NP_001007069.1  syntenin-1 isoform 2

      See identical proteins and their annotated locations for NP_001007069.1

      Status: REVIEWED

      Source sequence(s)
      BC013254, BG772269, U83463
      Consensus CDS
      CCDS47863.1
      UniProtKB/TrEMBL
      B4DQ93
      Related
      ENSP00000395351.2, ENST00000424270.6
      Conserved Domains (1) summary
      cd00992
      Location:106185
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    3. NM_001007069.2NP_001007070.1  syntenin-1 isoform 3

      See identical proteins and their annotated locations for NP_001007070.1

      Status: REVIEWED

      Source sequence(s)
      BC013254, BG772269, U83463
      Consensus CDS
      CCDS47862.1
      UniProtKB/TrEMBL
      B4DQ93
      Related
      ENSP00000409288.2, ENST00000447182.6
      Conserved Domains (1) summary
      cd00992
      Location:111190
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    4. NM_001007070.2NP_001007071.1  syntenin-1 isoform 3

      See identical proteins and their annotated locations for NP_001007071.1

      Status: REVIEWED

      Source sequence(s)
      BC013254, BG772269, U83463
      Consensus CDS
      CCDS47862.1
      UniProtKB/TrEMBL
      B4DQ93
      Conserved Domains (1) summary
      cd00992
      Location:111190
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    5. NM_001330537.2NP_001317466.1  syntenin-1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC068522, AK128645
      Consensus CDS
      CCDS83298.1
      UniProtKB/TrEMBL
      B4DQ93, G5EA09
      Related
      ENSP00000428184.1, ENST00000523483.5
      Conserved Domains (1) summary
      cd00992
      Location:132211
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    6. NM_001348339.2NP_001335268.1  syntenin-1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AK295198, BC013254
      Consensus CDS
      CCDS87610.1
      UniProtKB/TrEMBL
      B4DHN5, E9PBU7
      Related
      ENSP00000430730.1, ENST00000520168.5
      Conserved Domains (2) summary
      cd00136
      Location:56132
      PDZ; PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. ...
      cd00992
      Location:137210
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    7. NM_001348340.2NP_001335269.1  syntenin-1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC068522
      UniProtKB/TrEMBL
      B4DQ93
      Conserved Domains (1) summary
      cd00992
      Location:132211
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    8. NM_001348341.2NP_001335270.1  syntenin-1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC068522
      UniProtKB/TrEMBL
      B4DQ93
      Conserved Domains (1) summary
      cd00992
      Location:133212
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
    9. NM_005625.4NP_005616.2  syntenin-1 isoform 1

      See identical proteins and their annotated locations for NP_005616.2

      Status: REVIEWED

      Source sequence(s)
      BC013254, BG772269, U83463
      Consensus CDS
      CCDS6172.1
      UniProtKB/Swiss-Prot
      B2R5Q7, B4DUH3, B7ZLN2, O00173, O00560, O43391, Q14CP2
      UniProtKB/TrEMBL
      B4DQ93
      Related
      ENSP00000260130.4, ENST00000260130.9
      Conserved Domains (1) summary
      cd00992
      Location:112191
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      58553261..58582858
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047422077.1XP_047278033.1  syntenin-1 isoform X1

      UniProtKB/TrEMBL
      B4DQ93

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      58974408..59004011
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054360964.1XP_054216939.1  syntenin-1 isoform X1

      UniProtKB/TrEMBL
      B4DQ93